Shana Goffredi

Occidental College · Department of Biology

Persistent bacterial presence is believed to play an important role in host adaptation to specific niches that would otherwise be unavailable, including the exclusive consumption of blood by invertebrate parasites. Nearly all blood-feeding animals examined so far host internal bacterial symbionts that aid in some essential aspect of their nutrition...

Background Osedax, the deep-sea annelid found at sunken whalefalls, is known to host bacterial endosymbionts intracellularly in specialized roots, that help it feed exclusively on vertebrate bones. Past studies, however, have also made mention of external bacteria on their trunks. Here, we present an examination of the bacterial communities associa...

Osedax , the deep-sea annelid found at sunken whalefalls, is known to host Oceanospirillales bacterial endosymbionts intracellularly in specialized roots, that help it feed exclusively on vertebrate bones. Past studies, however, have also made mention of external bacteria on their trunks. During a 14-year study, we reveal a dynamic, yet persistent,...

Deep-sea chemosynthesis-based ecosystems support unique biological communities, but human impacts are an increasing threat. Understanding the life-history traits of species from deep-sea chemosynthesis-based ecosystems can help to develop adequate management strategies, as these can have impacts on ecological responses to changes in the environment...

Annelids have repeatedly evolved symbioses that allow them to colonise extreme ecological niches, like hydrothermal vents and whale falls. Yet, the genetic principles sustaining these symbiotic lifestyles remain unclear. Here we show that different genomic adaptations underpin the symbioses of phylogenetically related annelids with distinct nutriti...

The marine annelid Osedax has evolved a unique heterotrophic symbiosis that allows it to feed exclusively on sunken bones. Yet, the genetic and physiological principles sustaining this symbiosis are poorly understood. Here we show that Osedax frankpressi has a small, AT-rich genome shaped by extensive gene loss. While the Oceanospirillales endosymb...

Background Numerous deep-sea invertebrates, at both hydrothermal vents and methane seeps, have formed symbiotic associations with internal chemosynthetic bacteria in order to harness inorganic energy sources typically unavailable to animals. Despite success in nearly all marine habitats and their well-known associations with photosynthetic symbiont...

Relationships fueled by sulfide between deep‐sea invertebrates and bacterial symbionts are well known, yet the diverse overlapping factors influencing symbiont specificity are complex. For animals that obtain their symbionts from the environment, both host identity and geographic location can impact the ultimate symbiont partner. Bacterial symbiont...

Background Numerous deep-sea invertebrates have formed symbiotic associations with internal chemosynthetic bacteria in order to harness inorganic energy sources typically unavailable to most animals. Despite success in nearly all marine habitats and their well-known associations with photosynthetic symbionts, Cnidaria remain one of the only phyla w...

Deep-sea cold seeps are dynamic sources of methane release and unique habitats supporting ocean biodiversity and productivity. Here, we describe newly discovered animal-bacterial symbioses fueled by methane, between two species of annelid (a serpulid Laminatubus and sabellid Bispira ) and distinct aerobic methane-oxidizing bacteria belonging to the...

Deep-sea methane seeps are dynamic sources of greenhouse gas production and unique habitats supporting ocean biodiversity and productivity. Here, we demonstrate new animal-bacterial symbioses fueled by methane, between two undescribed species of annelid (a serpulid Laminatubus and sabellid Bispira) and distinct methane-oxidizing Methylococcales bac...

Deep-sea methane seeps are dynamic sources of greenhouse gas production and unique habitats supporting ocean biodiversity and productivity. Here, we demonstrate new animal-bacterial symbioses fueled by methane, between two undescribed species of annelid (a serpulid Laminatubus and sabellid Bispira) and distinct methane-oxidizing Methylococcales bac...

Abstract Background Darwin’s finches are a clade of 19 species of passerine birds native to the Galápagos Islands, whose biogeography, specialized beak morphologies, and dietary choices—ranging from seeds to blood—make them a classic example of adaptive radiation. While these iconic birds have been intensely studied, the composition of their gut mi...

The beetle genus Cephaloleia has evolved in association with tropical ginger plants and for many species their specific host plant associations are known. Here we show that the core microbiome of six closely related Costa Rican Cephaloleia species comprises only eight bacterial groups, including members of the Acinetobacter , Enterobacteriacea, Pse...

Table S1. Select key OTUs identified by SIMPER, representing notable taxonomic groups associated with six Cephaloleia species (n = 29 adult specimens and 5 eggs)–OTU#’s and colors match those on Figure 2. All microbial relative abundance data was calculated from 16S rRNA barcode sequencing results. Heat scales are added for ease of visualization an...

Table S2. 16S rRNA barcode data for all samples in this study. 16S rRNA barcode data for all samples in this study, at the family level, with and without Wolbachia included.

The beetle genus Cephaloleia has evolved in association with tropical ginger plants and for many species their specific host plant associations are known. Here we show that the core microbiome of six closely-related Costa Rican Cephaloleia species comprises only 8 bacterial groups, including members of the Acinetobacter , Enterobacteriacea, Pseudom...

The beetle genus Cephaloleia has evolved in association with tropical ginger plants and for many species their specific host plant associations are known. Here we show that the core microbiome of six closely-related Costa Rican Cephaloleia species comprises only 8 bacterial groups, including members of the Acinetobacter , Enterobacteriacea, Pseudom...

Phytophagous stink bugs are globally-distributed and many harbor vertically-inherited bacterial symbionts that are extracellular, yet little is known about how the symbiont's genomes have evolved under this transmission strategy. Genome reduction is common in insect intracellular symbionts but limited genome sampling of the extracellular symbionts...

We incorporate DNA sequences from a comprehensive sampling of taxa to provide an updated phylogeny of Osedax and discuss the remarkable diversity of this clade of siboglinids. We formally describe 14 new species of Osedax from Monterey Bay, California, USA, raising the total number of properly named Osedax species to 25. These new species had forme...

Forty years ago, scientists discovered an animal at the bottom of the ocean that changed forever how we view life on this planet. Abundant, thriving animals were not expected in the deep sea, due to the very low levels of organic carbon that sink down from above. The giant tubeworm Riftia pachyptila pays little attention to this problem, having ren...

Hydrothermal vent communities are distributed along mid-ocean spreading ridges as isolated patches. While distance is a key factor influencing connectivity among sites, habitat characteristics are also critical. The Pescadero Basin (PB) and Alarcón Rise (AR) vent fields, recently discovered in the southern Gulf of California, are bounded by previou...

In a variety of marine ecosystems, microbial eukaryotes play important ecological roles; however, our knowledge of their importance in deep-sea methane seep ecosystems is limited. Microbial eukaryotes have the potential to influence microbial community composition and diversity by creating habitat heterogeneity, and may contribute to carbon cycling...

Rubyspira osteovora is an unusual deep-sea snail from Monterey Canyon, CA. This group has only been found on decomposing whales and is thought to use bone as a novel source of nutrition. This study characterized the gut microbiome of R. osteovora, compared to the surrounding environment, as well as to other deep-sea snails with more typical diets....

We report identification and preliminary characterization of novel proteinaceous anticoagulants from two marine crustacea, Elthusa vulgaris and Phrixocephalus cincinnatus. We also propose naming them Occipodins in honor of the college where this undergraduate research has been initiated. The organisms were collected at 25-125 meters depth off the c...

Betaproteobacteria were the most common isolates from the water-filled tank of a Costa Rican bromeliad. Isolates included eight species from the orders Neisseriales and Burkholderiales, with close relatives recovered previously from tropical soils, wetlands, freshwater, or in association with plants. Compared to close relatives, the isolates displa...

Table S1. Phenotypic characteristics of bromeliad tank strains in comparison to other closely related members of the genus Burkholderia. Table S2. Phenotypic characteristics of bromeliad tank strains in comparison to other members of the genera Ralstonia and Cupriavidus. Table S3. Phenotypic characteristics of bromeliad tank strains in comparison...

RNA-Seq was used to examine the microbial, eukaryotic, and viral communities in water catchments (‘tanks’) formed by tropical bromeliads from Costa Rican. In total, transcripts with taxonomic affiliation to a wide array of bacteria, archaea, and eukaryotes, were observed, as well as RNA-viruses that appeared related to the specific presence of euka...

Termites and their microbial gut symbionts are major recyclers of lignocellulosic biomass. This important symbiosis is obligate but relatively open and more complex in comparison to other well-known insect symbioses such as the strict vertical transmission of Buchnera in aphids. The relative roles of vertical inheritance and environmental factors s...

Bdellovibrio bacteriovorus is a Gram-negative predator of other Gram-negative bacteria. Interestingly, Bdellovibrio bacteriovorus 109J cells grown in coculture with Escherichia coli ML-35 prey develop into a spatially organized two-dimensional film when located on a nutrient-rich surface. From deposition of 10 μl of a routine cleared coculture of B...

Interdomain symbioses with bacteria allow insects to take advantage of underutilized niches and provide the foundation for their evolutionary success in neotropical ecosystems. The gut microbiota of 13 micro-allopatric tropical pentatomid species, from a Costa Rican lowland rainforest, was characterized and compared with insect and host plant phylo...

We document a facultative Bartonella-like Rhizobiales bacterium in the giant tropical ant, Paraponera clavata. In a lowland tropical rainforest in Costa Rica, 59 colonies were assayed for the prevalence of the Bartonella-like bacterium (BLB), 14 of which were positive. We addressed three questions: First, how does the prevalence of BLB within colon...

An unusual symbiosis, first observed at ∼3000 m depth in the Monterey Submarine Canyon, involves gutless marine polychaetes of the genus Osedax and intracellular endosymbionts belonging to the order Oceanospirillales. Ecologically, these worms and their microbial symbionts have a substantial role in the cycling of carbon from deep-sea whale fall ca...

Recent investigations have demonstrated that unusually 'hairy' yeti crabs within the family Kiwaidae associate with two predominant filamentous bacterial families, the Epsilon and Gammaproteobacteria. These analyses, however, were based on samples collected from a single body region, the setae of pereopods. To more thoroughly investigate the microb...

‘Pliocardia' krylovata, sp. nov. (Bivalvia: Vesicomyidae: Pliocardiinae) is described from cold seeps off the coast of the Nicoya Peninsula, Costa Rica (700–1000 m depth). The phylogenetic position of ‘P.' krylovata was assessed by both morphological comparisons as well as nucleotide data from the cytochrome c oxidase I gene. Within the vesicomyids...

Leeches within the Piscicolidae are of great numerical and taxonomic importance, yet little is known about bacteria that associate with this diverse group of blood-feeding marine parasites of fish and elasmobranchs. We focused primarily on the bacteria from a deep-sea leech species of unknown identity, collected at ∼ 600 m depth in Monterey Canyon,...

Upon their initial discovery, hydrothermal vents and methane seeps were considered to be related but distinct ecosystems, with different distributions, geomorphology, temperatures, geochemical properties and mostly different species. However, subsequently discovered vents and seep systems have blurred this distinction. Here, we report on a composit...

Tropical epiphytic plants within the family Bromeliaceae are unusual in that they possess foliage capable of retaining water and impounded material. This creates an acidic (pH 3.5-6.5) and anaerobic (<1 ppm O(2)) environment suspended in the canopy. Results from a Costa Rican rainforest show that most bromeliads (n = 75/86) greater than ~20 cm in p...

Rhogocytes are morphologically distinct cells distributed throughout connective tissues of crustaceans and molluscs. Using light microscopy, rhogocytes of the vetigastropod Megathura crenulata were identified by their ovoid shape, and their cytoplasm filled with spherical inclusions which contained lysosomal enzymes, based on uptake of neutral red...

In a Costa Rican population of the bullet ant, Paraponera clavata, there is heterogeneity in the presence of Rhizobiales bacteria. Here we examine ecological and dietary factors that may affect the presence of Bartonella within a colony. Environmental conditions of the nesting sites and dietary preferences of colonies were evaluated, and diet manip...